Figure 3

Carrier ChIP-seq analyses on breast tumour core needle biopsies. A. Genome browser snapshots of ERα ChIP-seq on MCF7 cells (black) and breast cancer core needle biopsy samples with glycogen (blue) or mRNA/histones (red) as carriers. Tag count is shown on the Y-axis. Genomic locations are indicated. B. Genomic distributions of ERα binding events in MCF7 cells (top) and breast tumour biopsy samples with mRNA/histones as carrier (bottom). C. Motif analysis of ERα binding events on a core needle biopsy sample, with mRNA/histones as carrier. Indicated are the top 3 enriched motifs and p-values. D. Luminal enrichment for ERα carrier ChIP-seq genes. Genes, identified as ‘luminal’ or ‘basal’ signatures by Perou et al. [2] were analysed for proximal ERα binding events. Enrichment of ‘luminal’ over ‘basal’ genes was found. E. Genes, identified in D., were tested for correlation with recurrence-free survival, using Estrogen Receptor positive samples from a meta-analysis of breast cancer patients [19]. Expression of identified genes correlated with a favourable outcome after endocrine treatment.